Deutsches Zentrum für Neurodegenerative Erkrankungen

Jun 14 & 28, July 5 2023

9:00 am - 5:00 pm MESZ

Instructors: Margrit Klitz, Astrid Seidel

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Venusberg Campus 1/Gebäude 99, 53127 Bonn. Get directions with OpenStreetMap or Google Maps.

When: Jun 14 & 28, July 5 2023.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email margrit.klitz@dzne.de for more information.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1: June 14

Before Pre-workshop survey
09:00 Automating Tasks with the Unix Shell
10:15 First Morning break
10:30 Automating Tasks with the Unix Shell (Continued)
11:30 Second Morning break
11:45 Automating Tasks with the Unix Shell (Continued)
13:00 Lunch break
14:00 Version Control with Git
14:45 First Afternoon break
15:00 Version Control with Git (Continued)
15:45 Second Afternoon break
16:00 Version Control with Git (Continued)
16:45 Wrap-up
17:00 END

Day 2: June 28

09:00 R for Reproducible Scientific Analysis (Continued)
10:00 First Morning break
10:15 R for Reproducible Scientific Analysis (Continued)
11:15 Second Morning break
11:30 R for Reproducible Scientific Analysis (Continued)
12:30 Lunch break
13:30 R for Reproducible Scientific Analysis (Continued)
14:30 First Afternoon break
14:45 R for Reproducible Scientific Analysis (Continued)
15:45 Second Afternoon break
16:00 R for Reproducible Scientific Analysis(Continued)
16:45 Wrap-up
17:00 END

Day 3: July 5

09:00 Version Control with Git (Continued)
10:15 First Morning break
10:30 Version Control with Git (Continued)
11:30 Second Morning break
11:45 Version Control with Git (Continued)
13:00 Lunch break
14:00 Version Control with Git (Continued)
14:45 First Afternoon break
15:00 Version Control with Git (Continued)
15:45 Second Afternoon break
16:00 Version Control with Git (Continued)
16:30 Wrap-up
16:45 Post-workshop Survey
17:00 END

Setup

To participate in a Software Carpentry workshop, you will need access to a terminal, git, gitlab, R > 4.2 and RStudio > 2022. In addition, you will need an up-to-date web browser. We will set up a time and date, where you can come into the RS-IT-office, and we help you with any installations if necessary.